NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
Q04791 UniProt NPD GO	SASB_ANAPL	Fatty acyl-CoA hydrolase precursor, medium chain (EC 3.1.2.-) (Thioesterase B)	0.17	-	mit	0					557
O93499 UniProt NPD GO	KRF2_COLLI	Feather keratin Cos1-2 (F-ker)	0.17	-	nuc	0					100
P60815 UniProt NPD GO	FLVC2_RAT	Feline leukemia virus subgroup C receptor-related protein 2 (Calcium-chelate transporter) (CCT)	0.17	-	end	12	Cell membrane; multi-pass membrane protein (By similarity)				546
O04090 UniProt NPD GO	FER2_ARATH	Ferredoxin-2, chloroplast precursor	0.17	-	mit	0	Plastid; chloroplast				148
Q12333 UniProt NPD GO	FRE7_YEAST	Ferric reductase transmembrane component 7 (EC 1.16.1.7) (Ferric-chelate reductase 7)	0.17	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				629
Q2MHN1 UniProt NPD GO	FRIL_FELCA	Ferritin light chain (Ferritin L subunit)	0.17	-	cyt	0					174
P02791 UniProt NPD GO	FRIL_HORSE	Ferritin light chain (Ferritin L subunit)	0.17	-	cyt	0				1XZ3	174
P22508 UniProt NPD GO	FBRL_PHYPO	Fibrillarin (34 kDa nucleolar protein B-36) (Fragment)	0.17	-	cyt	0	Nucleus; nucleolus. Fibrillar region of the nucleolus				27
P15646 UniProt NPD GO	FBRL_YEAST	Fibrillarin (Nucleolar protein 1)	0.17	-	cyt	0	Nucleus; nucleolus. Fibrillar region of the nucleolus	nucleolus [IDA] small nuclear ribonucleoprotein complex [TAS] small nucleolar ribonucleoprotein complex [IPI]			327
Q29RY7 UniProt NPD GO	FGL2_BOVIN	Fibroleukin precursor (Fibrinogen-like protein 2)	0.17	-	mit	0	Secreted protein (By similarity)				441
Q91400 UniProt NPD GO	FINC_NOTVI	Fibronectin (FN) (Fragment)	0.17	-	cyt	0					190
Q80X90 UniProt NPD GO	FLNB_MOUSE	Filamin-B (FLN-B) (Beta-filamin) (Actin-binding-like protein) (ABP-280-like protein)	0.17	-	nuc	0	Cytoplasm; cell cortex. May localize also at actin stress fibers and within the Z-lines (By similari ...	focal adhesion [IDA] stress fiber [IDA]			2602
O75369 UniProt NPD GO	FLNB_HUMAN	Filamin-B (FLN-B) (Beta-filamin) (Actin-binding-like protein) (Thyroid autoantigen) (Truncated actin ...	0.17	-	nuc	0	Isoform 1: Cytoplasm; cell cortex. Isoform 2, isoform 3: Cytoplasm. Isoform 2 and isoform 3 are pred ...	actin cytoskeleton [TAS] integral to membrane [NAS]	603381		2602
O61491 UniProt NPD GO	FLOT1_DROME	Flotillin-1	0.17	-	cyt	0	Cell membrane; caveola; peripheral membrane protein. Membrane-associated protein of caveolae	flotillin complex [NAS]			426
O42305 UniProt NPD GO	FLOT2_CARAU	Flotillin-2 (Reggie-1) (REG-1)	0.17	-	mit	0	Membrane (By similarity). In neuronal cells; associated with GPI-anchored cell-adhesion molecules (B ...				428
Q6SI68 UniProt NPD GO	FSHB_MASCO	Follitropin beta chain precursor (Follicle-stimulating hormone beta subunit) (FSH-beta) (FSH-B)	0.17	-	exc	0	Secreted protein				130
O88618 UniProt NPD GO	FTCD_RAT	Formimidoyltransferase-cyclodeaminase (Formiminotransferase-cyclodeaminase) (FTCD) (58 kDa microtubu ...	0.17	-	nuc	0	Golgi apparatus	Golgi apparatus [IDA]		1TT9	541
O15552 UniProt NPD GO	FFAR2_HUMAN	Free fatty acid receptor 2 (G-protein coupled receptor 43)	0.17	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	603823		330
Q76EI6 UniProt NPD GO	FFAR2_RAT	Free fatty acid receptor 2 (G-protein coupled receptor 43)	0.17	-	end	7 *	Membrane; multi-pass membrane protein				330
P00636 UniProt NPD GO	F16P1_PIG	Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase 1) (FBPa ...	0.17	-	cyt	0				5FBP	337
P43394 UniProt NPD GO	K502_ACTCH	Fruit protein PKIWI502	0.17	-	mit	0					317
Q8R507 UniProt NPD GO	FCMD_MOUSE	Fukutin (EC 2.-.-.-)	0.17	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)	Golgi apparatus [IDA]			461
Q66IJ4 UniProt NPD GO	PIGM_XENTR	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Phosphatidylinositol- ...	0.17	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				419
Q500W7 UniProt NPD GO	PIGM_ARATH	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Phosphatidylinositol- ...	0.17	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				450
Q7SCL1 UniProt NPD GO	GWT1_NEUCR	GPI-anchored wall transfer protein 1 (EC 2.3.-.-)	0.17	+	end	12 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				504
P48596 UniProt NPD GO	GCH1_DROME	GTP cyclohydrolase I (EC 3.5.4.16) (GTP-CH-I) (Protein punch)	0.17	-	nuc	0					324
P32836 UniProt NPD GO	GSP2_YEAST	GTP-binding nuclear protein GSP2/CNR2	0.17	+	cyt	0	Nucleus	nucleus [IGI]			220
P36018 UniProt NPD GO	YPT52_YEAST	GTP-binding protein YPT52	0.17	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential). Also found in association with endoplasmi ...	late endosome [IMP]			234
P08760 UniProt NPD GO	KAD3_BOVIN	GTP:AMP phosphotransferase mitochondrial (EC 2.7.4.10) (Adenylate kinase 3) (AK3) (Adenylate kinase ...	0.17	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [ISS]		2AK3	226
Q96F15 UniProt NPD GO	GIMA5_HUMAN	GTPase, IMAP family member 5 (Immunity-associated nucleotide 4-like 1 protein) (Immunity-associated ...	0.17	-	cyt	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)		608086		307
P54803 UniProt NPD GO	GALC_HUMAN	Galactocerebrosidase precursor (EC 3.2.1.46) (GALCERase) (Galactosylceramidase) (Galactosylceramide ...	0.17	-	exc	1 *	Lysosome	lysosome [TAS]	606890		669
Q10979 UniProt NPD GO	FUT1_RABIT	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.17	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...				373
P11242 UniProt NPD GO	GALA_BOVIN	Galanin precursor [Contains: Galanin; Galanin message-associated peptide (GMAP)]	0.17	-	exc	1 *	Secreted protein				123
Q9QXQ6 UniProt NPD GO	GALP_RAT	Galanin-like peptide precursor	0.17	-	exc	0	Secreted protein				115
P19150 UniProt NPD GO	GBRA1_CHICK	Gamma-aminobutyric-acid receptor alpha-1 subunit precursor (GABA(A) receptor)	0.17	-	end	4	Membrane; multi-pass membrane protein				455
P47869 UniProt NPD GO	GBRA2_HUMAN	Gamma-aminobutyric-acid receptor alpha-2 subunit precursor (GABA(A) receptor)	0.17	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	137140		451
P26048 UniProt NPD GO	GBRA2_MOUSE	Gamma-aminobutyric-acid receptor alpha-2 subunit precursor (GABA(A) receptor)	0.17	-	end	4	Membrane; multi-pass membrane protein				451
P25123 UniProt NPD GO	GBRB_DROME	Gamma-aminobutyric-acid receptor subunit beta precursor (GABA(A) receptor) (Protein cyclodiene resis ...	0.17	-	end	4	Membrane; multi-pass membrane protein	integral to membrane [NAS]			606
Q99747 UniProt NPD GO	SNAG_HUMAN	Gamma-soluble NSF attachment protein (SNAP-gamma) (N-ethylmaleimide-sensitive factor attachment prot ...	0.17	-	nuc	0	Membrane; peripheral membrane protein (By similarity)	membrane fraction [NAS] mitochondrion [IDA]	603216		312
Q9CWZ7 UniProt NPD GO	SNAG_MOUSE	Gamma-soluble NSF attachment protein (SNAP-gamma) (N-ethylmaleimide-sensitive factor attachment prot ...	0.17	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				312
Q64448 UniProt NPD GO	CXA3_MOUSE	Gap junction alpha-3 protein (Connexin-46) (Cx46)	0.17	-	end	3 *	Membrane; multi-pass membrane protein	gap junction [IDA]			416
P35212 UniProt NPD GO	CXA4_HUMAN	Gap junction alpha-4 protein (Connexin-37) (Cx37)	0.17	-	end	3 *	Membrane; multi-pass membrane protein	gap junction [TAS] integral to plasma membrane [TAS]	121012		332
Q58D78 UniProt NPD GO	CXB3_BOVIN	Gap junction beta-3 protein (Connexin-31) (Cx31)	0.17	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				270
Q689Z7 UniProt NPD GO	PEPC_MONDO	Gastricsin precursor (EC 3.4.23.3) (Pepsinogen C)	0.17	-	exc	0	Secreted protein				391
Q863C3 UniProt NPD GO	GRP_BOVIN	Gastrin-releasing peptide precursor (GRP) [Contains: Neuromedin C (GRP-10) (GRP-(18-27))] (Fragment) ...	0.17	-	nuc	0	Secreted protein				126
P18712 UniProt NPD GO	ZG16_XENLA	Gastrula zinc finger protein XLCGF16.1 (Fragment)	0.17	-	nuc	0	Nucleus (Potential)				112
O95749 UniProt NPD GO	GGPPS_HUMAN	Geranylgeranyl pyrophosphate synthetase (GGPP synthetase) (GGPPSase) (Geranylgeranyl diphosphate syn ...	0.17	-	cyt	0	Cytoplasm	soluble fraction [IDA]	606982	2FVI	300
Q9SQ80 UniProt NPD GO	G2OX1_PEA	Gibberellin 2-beta-dioxygenase 1 (EC 1.14.11.13) (Gibberellin 2-beta-hydroxylase 1) (Gibberellin 2-o ...	0.17	-	mit	0					327
O64692 UniProt NPD GO	G2OX3_ARATH	Gibberellin 2-beta-dioxygenase 3 (EC 1.14.11.13) (Gibberellin 2-beta-hydroxylase 3) (Gibberellin 2-o ...	0.17	+	cyt	0					335
O60234 UniProt NPD GO	GMFG_HUMAN	Glia maturation factor gamma (GMF-gamma)	0.17	+	cyt	0			604104		142

You are viewing entries 54301 to 54350 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.